Molecular dynamics simulations of complex systems.
Advanced simulation techniques with enhanced sampling. The non equilibrium
approach. Alchemical technologies for binding affinities in host-guest
systems.
Computational Chemistry (II ed.)
CJ Cramer
Wiley
ISBN 0-470-09182-7
Lecture notes
Learning Objectives
Computational methods are currently of paramount importance for the understanding the properties of complex systems. This course is aimed at training students on modern computational methods and computational tools. The students will be able to understand the approximations that underpin these methods, the accuracy that can be achieved, and to compare the results with experimental data.
Prerequisites
none
Teaching Methods
Class lectures.
Hands-on exercises on computer simulations
Type of Assessment
Oral examination
Course program
Restricted and unrestricted Hartree Fock method. Correlation energy and post-Hartree Fock techniques. Density functional theory. Ab initio Calculations of molecular properties.
Ab initio simulations.
Thermodynamic ensembles. Microcanonical, Canonical and
isothermal-isobaric ensembles. Force fields in Molecular
Mechanics. Molecular dynamics of complex molecular systems. Periodic
Boundary conditions ed electrostatic interactions. Numerical
integration of the classical equations of motion. Constant temperature
and constant pressure simulations. Advanced techniques: enhanced
sampling simulation; Replica exchange methods, metadynamics. Non
equilibrium simulation techniques. Crooks theorem and Jarzynski
theorem. Alchemical methodologies for binding affinities in Drug
receptor systems.